It took a long time, but with patch ESXi-5.5.0-20150104001-standard (2099271) VMware managed to fix the Changed Block Tracking (CBT) Bug for ESXi 5.5 together with a number of other known issues.
Here is an excerpt from the release note:
When you use backup software that uses the Virtual Disk Development Kit (VDDK) API call QueryChangedDiskAreas(), the list of allocated disk sectors returned might be incorrect and incremental backups might appear to be corrupt or missing. A message similar to the following is written to vmware.log:
DISKLIB-CTK: Resized change tracking block size from XXX to YYY
For more information, see KB 2090639.
A fix for ESXi 5.0 and 5.1 is available since December, 15th: Changed Block Tracking (CBT) Bug fixed for ESXi 5.0 and ESXi 5.1